To evaluate the effect of micro-nutrients spraying on some agronomic characteristics of the safflower (Carthamus tinctorius L. cv. Isfahan landrace), under different cropping systems, an experiment was carried out as split plot based on randomized complete block design with three replications in 2011. Experimental treatments were including: cropping systems (high, medium, low input and ecological cropping systems) as main plots and micro-nutrients (no foliar application, 2 per thousand zinc chelate, 3 per thousand manganese chelate, 2 per thousand zinc chelate + 3 per thousand manganese chelate, water spraying) as sub plot. Results showed that the effect of cropping system and micronutrient spraying on stem diameter, number of branches in plant, capsule diameter, weight of capsule, stem dry weight and seed oil percentage was significant, and also interaction effect between cropping system and micronutrient spraying on grain yield and plant height was significant. The highest yield of seed (4115.6 kg/ha) and plant height (90.62cm) was obtained from high input cropping system and zinc spraying. The minimum grain yield (1540.3 kg/ha) was obtained in plants sprayed with water in ecological cropping system. Stem diameter, number of branches per plant and capsule diameter increased in treated plants with both zinc and manganese. But, the highest weight of capsule and dried weight of stem were affected only by foliar application of zinc. Spraying plants with zinc caused to increase the yield of safflower in medium input as well as high input system.